RMarkdownDemo
liang kuang
2017-05-02
1 Load the packages
suppressPackageStartupMessages({
library(knitr)
library(pander)
library(dygraphs)
library(zoo)
library(Quandl)
library(ggplot2)
})2 R Markdown Layout
3 Global settings
Before writing your RMarkdown document, user can specify the global settings for the global environment. For example, setting whether to echo your R code and show the code/results etc. in the document. You can either set the options globally or for individual code blocks.
## global setting for all blocks
{r setup, include = FALSE}
knitr::opts_chunk$set(echo = TRUE)
## setting for individual code block
{r chuck_name, echo = FALSE, results = "hide", include = TRUE}
x <- rnorm(100)
y <- 2*x + rnorm(100)If you want all the figures take the same amount of space, use the following commands:
{r global_options, include = FALSE}
knitr::opts_chunk$set(fig.width = 12, fig.height = 8, fig.path = 'Figs/',
echo = FALSE, warning = FALSE, message = FALSE)
# While setting figure path, the '/' is very import. Also, you can individually change the settings for your figure windows. This will overwrite global settings. This is very convenient especially when you have images for different data size. For example, by specifying ‘fig.with’ and ‘fig.height’:
{r scatterplot, fig.width = 8, fig.height = 6}
plot(x,y)4 Create Paragraphs With Styles
4.1 Headers
# Header 1
## Header 2
### Header 34.2 Lists
4.2.1 Unordered List
* Item 1
* Item 2
+ Item 2a
+ Item 2bThis is the example output for Unordered Lists:
- Item 1
- ITem 2
- Item 2a
- Item 2b
4.2.2 Ordered List
1. Item 1
2. Item 2
3. Item 3
+ Item 3a
+ Item 3bThis is the example output for ordered list:
- Item 1
- Item 2
- Item 3
- Item 3a
- Item 3b
4.3 Emphasis
From time to time, we might want to emphasize our text either using {**bold**} or {*italic*}. Also, we can change the text color by using styles. We can say roses are red, violets are blue by using command <span style="color:red">red</span> and <span style="color:blue">blue</span> repsectively.
5 Embed code chunk, inline code and run R code
5.1 R Code Chunks
R code will be evaluated and printed
size = 750
x = as.data.frame(matrix(runif(14*size),ncol=14))
head(x)## V1 V2 V3 V4 V5 V6 V7
## 1 0.2826153 0.27619028 0.2147521 0.1365030 0.6038595 0.65325169 0.03552247
## 2 0.7671862 0.86837233 0.3679879 0.9271022 0.8745636 0.86130532 0.22411733
## 3 0.6158803 0.04620431 0.1696513 0.1200033 0.1273721 0.49674987 0.88338218
## 4 0.3449832 0.84746335 0.0284731 0.9341338 0.5529134 0.02383497 0.86995211
## 5 0.8399923 0.33462644 0.4105045 0.5085341 0.4479008 0.89362047 0.20574309
## 6 0.1708209 0.73196337 0.1178317 0.9711985 0.5453431 0.52892483 0.83249019
## V8 V9 V10 V11 V12 V13
## 1 0.8295534 0.6976623 0.04591954 0.7829101176 0.97276066 0.6032213
## 2 0.4352041 0.4899945 0.59168662 0.5728689663 0.35471090 0.9498747
## 3 0.9384053 0.9173653 0.49125009 0.1842383607 0.34319323 0.7180012
## 4 0.7877587 0.2565447 0.26821289 0.4111792219 0.04415267 0.4957210
## 5 0.7301219 0.6665794 0.70052458 0.0004130306 0.35711218 0.9748445
## 6 0.6704121 0.6650134 0.16385878 0.0552149068 0.83045260 0.2445284
## V14
## 1 0.467044100
## 2 0.792592079
## 3 0.657415150
## 4 0.351200123
## 5 0.006000512
## 6 0.6400005205.2 Embed Code Chunk
In RMarkdown, we can symply embed a chunk of code by using
x = matrix(runif(14*size),ncol=14)
y = 10 * sin(pi*x[,1]*x[,2]) + 20*(x[,3]-0.5)**2 + 10*x[,4] + 5*x[,5] + runif(1,0,1)
x[,11:14] = x[,1:4] + matrix(runif(4*size,min = 0, max = 0.025),ncol=4)5.3 Inline Code
Inline code can be excecuted using two plus two equals 4 using two plus two equals 4
6 Generate R Graphics and Table
data=data.frame(value=rnorm(10000))
# Basic histogram
ggplot(data, aes(x=value)) + geom_histogram()## `stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
# Custom Binning. I can just give the size of the bin
ggplot(data, aes(x=value)) + geom_histogram(binwidth = 0.05)
# Uniform color
ggplot(data, aes(x=value)) +
geom_histogram(binwidth = 0.2, color="white", fill=rgb(0.2,0.7,0.1,0.4) ) 
# Proportional color
ggplot(data, aes(x=value)) +
geom_histogram(binwidth = 0.2, aes(fill = ..count..) )
7 Embed images, hyperlink, and advanced items (animation, interactive maps etc.)
Images on the web or local files in the same directory:
IHS Markit
8 Embed Mathematic Equations
There are two ways to embed equations using LaTex format: inline equation and block equations.
8.1 Inline Equation
This is an example of inline equation using $ quotes. $10sin(\pi x_1x_2)$ ==> \(10sin(\pi x_1x_2)\)
8.2 Display Equations
This is an example of display equations using $$ quotes. $$y = 10sin(\pi x_1x_2) + 20(x_3-0.5)^2 + 10x_4+5x_5+\epsilon$$=> \[y = 10sin(\pi x_1x_2) + 20(x_3-0.5)^2 + 10x_4+5x_5+\epsilon\]
9 Tables
R Markdown can also create simple tables very easily by following syntax:
First Header | Second Header
------------ | -------------
Content Cell | Content Cell
Content Cell | Content Cell
Content Cell | Content Cell
Reference Style Links and ImagesHere is an example output:
| Name | Age | Hobby |
|---|---|---|
| Jack | 22 | Travel |
| Adam | 33 | Movie |
| Judy | 25 | Party |
10 Auto Cite References
In RMarkdown, we can also easily cite our references by coupling with reference managers. For example: Application written in the R programming language (R Core Team 2016) using the Shiny framework (Tutorialspoint 2015).
11 Advanced Features
RMarkdown can also embed advanced objects into its HTML output: video, interactive graphics etc. Here are some examples of the advanced features:
11.1 Interactive graphs
11.1.1 Interactive time series
brent <- Quandl("EIA/PET_RBRTE_D", collapse="monthly", type="ts")
dygraph(brent, main = "Brent Spot Prices") %>% dyRangeSelector() %>%
dyAxis("y", label = "US $/Barrel") %>%
dySeries("V1", label = "Brent ($/Barrel)") %>%
dyLegend(show = "follow")11.1.2 GeoSpatial Visualization
library(leaflet)
m <- leaflet() %>%
addTiles() %>% # Add default OpenStreetMap map tiles
addMarkers(lng=-77.003, lat=38.9, popup="IHS MARKIT")
m # Print the map11.1.3 rbokeh
library(rbokeh)
figure() %>%
ly_points(Sepal.Length, Sepal.Width, data = iris,
color = Species, glyph = Species,
hover = list(Sepal.Length, Sepal.Width))11.1.4 networkViz
library(visNetwork)
nodes <- data.frame(id = 1:6, title = paste("node", 1:6),
shape = c("dot", "square"),
size = 10:15, color = c("blue", "red"))
edges <- data.frame(from = 1:5, to = c(5, 4, 6, 3, 3))
visNetwork(nodes, edges) %>%
visOptions(highlightNearest = TRUE, nodesIdSelection = TRUE)11.1.5 plotly
library(ggplot2)
library(plotly)##
## Attaching package: 'plotly'## The following object is masked from 'package:ggplot2':
##
## last_plot## The following object is masked from 'package:stats':
##
## filter## The following object is masked from 'package:graphics':
##
## layoutp <- ggplot(data = diamonds, aes(x = cut, fill = clarity)) +
geom_bar(position = "dodge")
ggplotly(p)## Warning: We recommend that you use the dev version of ggplot2 with `ggplotly()`
## Install it with: `devtools::install_github('hadley/ggplot2')`11.1.6 networkD3
# Load data
library(networkD3)##
## Attaching package: 'networkD3'## The following object is masked from 'package:leaflet':
##
## JSdata(MisLinks)
data(MisNodes)
# Plot
forceNetwork(Links = MisLinks, Nodes = MisNodes,
Source = "source", Target = "target",
Value = "value", NodeID = "name",
Group = "group", opacity = 0.8)URL <- paste0(
"https://cdn.rawgit.com/christophergandrud/networkD3/",
"master/JSONdata//flare.json")
## Convert to list format
Flare <- jsonlite::fromJSON(URL, simplifyDataFrame = FALSE)
# Use subset of data for more readable diagram
Flare$children = Flare$children[1:3]
radialNetwork(List = Flare, fontSize = 10, opacity = 0.9)diagonalNetwork(List = Flare, fontSize = 10, opacity = 0.9)hc <- hclust(dist(USArrests), "ave")
dendroNetwork(hc, height = 600)11.2 Video
htmltools::includeHTML("embed_video_Rmarkdown.html")REFERENCES
R Core Team. 2016. “R: A Language and Envirnoment for Statistical Computing.” Journal Article. http:///www.R-project.org.
Tutorialspoint. 2015. “Perl Programming.”